Merge pull request #371 from PDXFinder/beta

Beta
PDCMFinder · Oct 28, 2020 · c5bdf87 · c5bdf87
2 parents 43ed7a9 + b05b37e
commit c5bdf87
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Showing 191 changed files with 3,975 additions and 7,606 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,5 @@
+log/
+
 *.class
 */target/
 

diff --git a/admin/pom.xml b/admin/pom.xml
@@ -24,6 +24,7 @@
             <groupId>org.pdxfinder</groupId>
             <artifactId>data-services</artifactId>
         </dependency>
+
         <dependency>
             <groupId>org.pdxfinder</groupId>
             <artifactId>data-model</artifactId>
@@ -39,80 +40,22 @@
             <artifactId>spring-boot-starter-actuator</artifactId>
         </dependency>
 
-        <!--<dependency>
-            <groupId>org.springframework.boot</groupId>
-            <artifactId>spring-boot-starter-thymeleaf</artifactId>
-        </dependency>
-
-        <dependency>
-            <groupId>org.webjars</groupId>
-            <artifactId>bootstrap</artifactId>
-            <version>3.3.7</version>
-        </dependency>
-
         <dependency>
-            <groupId>org.webjars</groupId>
-            <artifactId>font-awesome</artifactId>
-            <version>4.7.0</version>
+            <groupId>org.neo4j</groupId>
+            <artifactId>neo4j-ogm-bolt-driver</artifactId>
+            <version>3.1.20</version>
         </dependency>
 
         <dependency>
-            <groupId>org.webjars</groupId>
-            <artifactId>animate.css</artifactId>
-            <version>3.5.2</version>
+            <!-- WARNING, do not update db engine (stable: 1.4.197) cause compatibility issues, see https://github.com/h2database/h2database/issues/2078 -->
+            <groupId>com.h2database</groupId>
+            <artifactId>h2</artifactId>
+            <version>1.4.197</version>
         </dependency>
-
-        <dependency>
-            <groupId>org.webjars.bower</groupId>
-            <artifactId>amcharts3</artifactId>
-            <version>3.21.3</version>
-        </dependency>
-
-        <dependency>
-            <groupId>org.webjars</groupId>
-            <artifactId>webjars-locator</artifactId>
-        </dependency>-->
-
     </dependencies>
 
     <build>
         <plugins>
-            <!--<plugin>
-                <groupId>org.codehaus.mojo</groupId>
-                <artifactId>exec-maven-plugin</artifactId>
-                <version>1.6.0</version>
-                <executions>
-                    <execution>
-                        <id>install-dependencies</id>
-                        <phase>validate</phase>
-                        <goals>
-                            <goal>exec</goal>
-                        </goals>
-                        <configuration>
-                            <executable>${npm.executable}</executable>
-                            <workingDirectory>src/main/app-ui</workingDirectory>
-                            <arguments>
-                                <argument>install</argument>
-                            </arguments>
-                        </configuration>
-                    </execution>
-                    <execution>
-                        <id>build-angular-app</id>
-                        <phase>validate</phase>
-                        <goals>
-                            <goal>exec</goal>
-                        </goals>
-                        <configuration>
-                            <executable>ng</executable>
-                            <workingDirectory>src/main/app-ui</workingDirectory>
-                            <arguments>
-                                <argument>build</argument>
-                            </arguments>
-                        </configuration>
-                    </execution>
-                </executions>
-
-            </plugin>-->
             <plugin>
                 <groupId>org.springframework.boot</groupId>
                 <artifactId>spring-boot-maven-plugin</artifactId>
@@ -127,21 +70,4 @@
         </plugins>
     </build>
 
-    <!-- Windows requires different command line -->
-    <!--<profiles>
-        <profile>
-            <id>platform-windows</id>
-            <activation>
-                <os>
-                    <family>windows</family>
-                </os>
-            </activation>
-            <properties>
-                <npm.executable>npm.cmd</npm.executable>
-                <grunt.executable>grunt.cmd</grunt.executable>
-                <bower.executable>bower.cmd</bower.executable>
-            </properties>
-        </profile>
-    </profiles>-->
-
 </project>
diff --git a/admin/src/main/java/org/pdxfinder/controllers/AjaxController.java b/admin/src/main/java/org/pdxfinder/controllers/AjaxController.java
@@ -5,11 +5,11 @@
 import com.fasterxml.jackson.dataformat.csv.CsvMapper;
 import com.fasterxml.jackson.dataformat.csv.CsvSchema;
 import org.pdxfinder.rdbms.dao.MappingEntity;
-import org.pdxfinder.services.zooma.ZoomaEntity;
 import org.pdxfinder.services.MappingService;
 import org.pdxfinder.services.UtilityService;
 import org.pdxfinder.services.dto.PaginationDTO;
 import org.pdxfinder.services.mapping.CSVHandler;
+import org.pdxfinder.services.zooma.ZoomaEntity;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -20,6 +20,7 @@
 import org.springframework.web.multipart.MultipartFile;
 
 import javax.servlet.http.HttpServletResponse;
+import java.io.IOException;
 import java.util.*;
 
 
@@ -127,7 +128,7 @@ public ResponseEntity<?> getMappingStatSummary(@RequestParam(value = "entity-typ
      * Bulk update of Records
      */
     @PutMapping("/mappings")
-    public ResponseEntity<?> editListOfEntityMappings(@RequestBody List<MappingEntity> submittedEntities) {
+    public ResponseEntity<?> editListOfEntityMappings(@RequestBody List<MappingEntity> submittedEntities) throws IOException {
 
         List data = mapper.convertValue(submittedEntities, List.class);
         log.info(data.toString());

diff --git a/admin/src/main/java/org/pdxfinder/controllers/TransController.java b/admin/src/main/java/org/pdxfinder/controllers/TransController.java
@@ -4,11 +4,11 @@
 import org.apache.commons.collections4.ListUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.pdxfinder.rdbms.dao.MappingEntity;
-import org.pdxfinder.rdbms.repositories.MappingEntityRepository;
-import org.pdxfinder.services.UtilityService;
-import org.pdxfinder.services.TransformerService;
 import org.pdxfinder.rdbms.dao.PdmrPdxInfo;
 import org.pdxfinder.rdbms.dao.PdxInfo;
+import org.pdxfinder.rdbms.repositories.MappingEntityRepository;
+import org.pdxfinder.services.TransformerService;
+import org.pdxfinder.services.UtilityService;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;

diff --git a/admin/src/main/resources/application.properties b/admin/src/main/resources/application.properties
@@ -17,7 +17,6 @@ spring.thymeleaf.cache=false
 server.port=8081
 
 mappings.diagnosis.file = "";
-
 mappings.mappedTermUrl=http://localhost/data/mappings.json
 
 ## H2 Config
@@ -26,7 +25,6 @@ spring.h2.console.path=/db-admin/console
 spring.h2.console.settings.web-allow-others=true
 
 # NON-GRAPH Datasource Config properties
-#${HOME}
 spring.datasource.url=jdbc:h2:${data-dir}/h2-db/data;AUTO_SERVER=true;DB_CLOSE_ON_EXIT=FALSE
 spring.datasource.username=neo4j
 spring.datasource.password=neo5j
@@ -35,8 +33,11 @@ spring.h2.console.settings.trace=true
 ## Hibernate Config
 spring.jpa.hibernate.ddl-auto=update
 
+# Enable certain actuator endpoints
+management.endpoint.env.enabled=true
+management.endpoints.web.base-path=/manage
+management.endpoints.web.exposure.include=env
 
 # root directory for local data feeds
 data-dir=/nfs/web-hx/mouseinformatics/pdx/finderroot
 
-#${HOME}/PDXFinder
diff --git a/data-model/pom.xml b/data-model/pom.xml
@@ -3,6 +3,21 @@
          xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
          xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <modelVersion>4.0.0</modelVersion>
+    <dependencies>
+        <dependency>
+            <groupId>com.google.code.gson</groupId>
+            <artifactId>gson</artifactId>
+            <version>2.8.2</version>
+            <scope>compile</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.neo4j</groupId>
+            <artifactId>neo4j-ogm-embedded-driver</artifactId>
+            <version>3.1.20</version>
+            <scope>test</scope>
+        </dependency>
+
+    </dependencies>
 
     <parent>
         <groupId>org.pdxfinder</groupId>
@@ -14,20 +29,4 @@
     <artifactId>data-model</artifactId>
     <packaging>jar</packaging>
 
-    <dependencies>
-
-        <dependency>
-            <groupId>org.neo4j</groupId>
-            <artifactId>neo4j-ogm-embedded-driver</artifactId>
-            <scope>test</scope>
-            <version>2.1.1</version>
-        </dependency>
-
-<!--        <dependency>
-            <groupId>org.springframework.boot</groupId>
-            <artifactId>spring-boot-starter-data-rest</artifactId>
-        </dependency>-->
-
-    </dependencies>
-
 </project>
diff --git a/data-model/src/main/java/org/pdxfinder/graph/dao/CurrentTreatment.java b/data-model/src/main/java/org/pdxfinder/graph/dao/CurrentTreatment.java
@@ -1,6 +1,7 @@
 package org.pdxfinder.graph.dao;
 
-import org.neo4j.ogm.annotation.GraphId;
+import javax.persistence.GeneratedValue;
+import javax.persistence.Id;
 import org.neo4j.ogm.annotation.NodeEntity;
 
 /*
@@ -9,7 +10,7 @@
 @NodeEntity
 public class CurrentTreatment {
 
-    @GraphId
+    @Id @GeneratedValue
     private Long id;
 
     private String name;

diff --git a/data-model/src/main/java/org/pdxfinder/graph/dao/DataProjection.java b/data-model/src/main/java/org/pdxfinder/graph/dao/DataProjection.java
@@ -1,6 +1,7 @@
 package org.pdxfinder.graph.dao;
 
-import org.neo4j.ogm.annotation.GraphId;
+import javax.persistence.GeneratedValue;
+import javax.persistence.Id;
 import org.neo4j.ogm.annotation.NodeEntity;
 
 /*
@@ -9,7 +10,7 @@
 @NodeEntity
 public class DataProjection {
 
-    @GraphId
+    @Id @GeneratedValue
     private Long id;
 
     private String label;

diff --git a/data-model/src/main/java/org/pdxfinder/graph/dao/Drug.java b/data-model/src/main/java/org/pdxfinder/graph/dao/Drug.java
@@ -1,6 +1,7 @@
 package org.pdxfinder.graph.dao;
 
-import org.neo4j.ogm.annotation.GraphId;
+import javax.persistence.GeneratedValue;
+import javax.persistence.Id;
 import org.neo4j.ogm.annotation.NodeEntity;
 
 /*
@@ -18,7 +19,7 @@ public class Drug {
      * @param synonyms                  Synonyms of the drug
      */
 
-    @GraphId
+    @Id @GeneratedValue
     private Long id;
 
     private String name;

diff --git a/data-model/src/main/java/org/pdxfinder/graph/dao/ExternalDataSource.java b/data-model/src/main/java/org/pdxfinder/graph/dao/ExternalDataSource.java
@@ -1,6 +1,7 @@
 package org.pdxfinder.graph.dao;
 
-import org.neo4j.ogm.annotation.GraphId;
+import javax.persistence.GeneratedValue;
+import javax.persistence.Id;
 import org.neo4j.ogm.annotation.NodeEntity;
 
 import java.util.Date;
@@ -12,7 +13,7 @@
 @NodeEntity
 public class ExternalDataSource {
 
-    @GraphId
+    @Id @GeneratedValue
     private Long id;
 
     private String name;

diff --git a/data-model/src/main/java/org/pdxfinder/graph/dao/ExternalUrl.java b/data-model/src/main/java/org/pdxfinder/graph/dao/ExternalUrl.java
@@ -1,7 +1,8 @@
 package org.pdxfinder.graph.dao;
 
 
-import org.neo4j.ogm.annotation.GraphId;
+import javax.persistence.GeneratedValue;
+import javax.persistence.Id;
 import org.neo4j.ogm.annotation.NodeEntity;
 
 /**
@@ -10,7 +11,7 @@
 @NodeEntity
 public class ExternalUrl {
 
-    @GraphId
+    @Id @GeneratedValue
     private Long id;
     private String type;
     private String url;

diff --git a/data-model/src/main/java/org/pdxfinder/graph/dao/Histology.java b/data-model/src/main/java/org/pdxfinder/graph/dao/Histology.java
@@ -1,6 +1,7 @@
 package org.pdxfinder.graph.dao;
 
-import org.neo4j.ogm.annotation.GraphId;
+import javax.persistence.GeneratedValue;
+import javax.persistence.Id;
 import org.neo4j.ogm.annotation.NodeEntity;
 import org.neo4j.ogm.annotation.Relationship;
 
@@ -13,7 +14,7 @@
 @NodeEntity
 public class Histology {
 
-    @GraphId
+    @Id @GeneratedValue
     Long id;
 
     @Relationship(type = "HAS_IMAGE")

diff --git a/data-model/src/main/java/org/pdxfinder/graph/dao/Image.java b/data-model/src/main/java/org/pdxfinder/graph/dao/Image.java
@@ -1,6 +1,7 @@
 package org.pdxfinder.graph.dao;
 
-import org.neo4j.ogm.annotation.GraphId;
+import javax.persistence.GeneratedValue;
+import javax.persistence.Id;
 import org.neo4j.ogm.annotation.NodeEntity;
 
 /**
@@ -9,7 +10,7 @@
 @NodeEntity
 public class Image {
 
-    @GraphId
+    @Id @GeneratedValue
     Long id;
 
     private String url;

diff --git a/data-model/src/main/java/org/pdxfinder/graph/dao/Marker.java b/data-model/src/main/java/org/pdxfinder/graph/dao/Marker.java
@@ -3,9 +3,9 @@
 import org.apache.commons.lang3.StringUtils;
 import org.neo4j.ogm.annotation.Index;
 import org.neo4j.ogm.annotation.NodeEntity;
+
 import javax.persistence.GeneratedValue;
 import javax.persistence.Id;
-import java.util.Arrays;
 import java.util.HashSet;
 import java.util.Set;
 

diff --git a/data-model/src/main/java/org/pdxfinder/graph/dao/MarkerAssociation.java b/data-model/src/main/java/org/pdxfinder/graph/dao/MarkerAssociation.java
@@ -24,7 +24,7 @@ public class MarkerAssociation {
     private String molecularDataString;
     private int dataPoints = 0;
 
-    private List<MolecularData> molecularDataList = new ArrayList<>();
+    private List<MolecularData> molecularDataList;
 
     public MarkerAssociation() {
         molecularDataList = new ArrayList<>();
@@ -39,7 +39,8 @@ else return new ObjectMapper().readValue(
     }
 
     public void encodeMolecularData(){
-        molecularDataString = new Gson().toJson(molecularDataList);
+        Gson gson = new Gson();
+        molecularDataString = gson.toJson(molecularDataList);
         dataPoints = molecularDataList.size();
         molecularDataList = Collections.emptyList();
     }